Projet MICRORESCUE (European Research Council Consolidator Award 2023-2028)
MicroRescue : Resolving mechanisms of microbiome rescue to promote resilience to climate change (contact : A. Shade)
Earth’s climate crisis threatens to disrupt ecosystem services and destabilize food security. Communities of microorganisms, called microbiomes, provide critical functions that provide feedback on climate and support soil and plant health. However, recovering microbial populations and functions lost after environmental disturbances may be possible. This research will elaborate strategies that leverage the selective reactivation of dormant microbes to drive resilient plant and soil systems. Because microbial dormancy is extensive in the soil, reactivation offers access to untapped biodiversity and could provide solutions for maintaining functions in ecosystems affected by climate change. This research will first investigate the capacity of dormant soil bacteria to rescue microbiomes in a changing climate and, second, the utility of bacterial reactivation to support plant resilience to climate change. This work will provide general insights into microbiome resilience and identify microbial targets for interventions to support soils and crops facing climate change. https://ashley17061.wixsite.com/shadelab
Projet Into the Waste (GRAINE-ADEME 2023-2024)
Study and optimization of on-site composting of kitchen and table waste to ensure the sanitary quality of composts. (contact : S. Nazaret). This project follows on from the MicrobioWaste project, which studied the safety of catering waste with a view to using it as a biofertiliser. Here, we are looking at the dynamics of a number of pathogens in composted catering waste and linking this to changes in the diversity of microbial communities.
Projet AMBITOME ( FR BioEEnViS 2023-2024)
Amoebae and global warming: role in the emergence of environmental antibiotic resistance (contact : T. Meyer). Through this project, we aim to assess the impact of global warming on i°) the composition of the amoebic microbiome, ii°) the antimicrobial resistance and production functions of this microbiome.
Projet SARA (ANR 2021-2024)
Surveillance of Emerging Pathogens and Antibiotic Resistance (contact : T. Vogel). Appropriate methods for wastewater-based epidemiology (WBE), and a better understanding of the fate of pathogenic viruses and antibiotic resistant bacteria from the sources to river basins and estuaries are urgently required. Our project will determine the prevalence of pathogenic viruses (including SARS-CoV-2), microbial indicators, antibiotic resistance, and microbial source tracking (MST) markers in wastewater, surface water, coastal sea waters, sediment and bivalve molluscan shellfish (BMS) in catchments located in different climate areas (SE, DE, FR, ES, PT, IL, MZ, and UG). The project aims are: (i) method harmonization, (ii) SARS-CoV-2 detection in raw wastewater as biomarker of COVID-19 cases,(iii) enteric viruses, antibiotic resistances and MST markers monitoring in aquatic environments, (iv) evaluation of sediments and BMS as integral reservoirs, (v) determination of the impact of climate and extreme weather events, and (vi) microbial risk assessment for water resources.
The problem addressed relates to how pathogens in sewage enter rivers and if sediments become a reservoir where survival might be improved. This will have significant benefits as surveillance will demonstrate that we need improved treatment options to stop all bacteria, ARBs, viruses entering the environment and risking human exposure via recreation activities, irrigation of food crops and via abstraction. Such results are of particular relevance to solve environmental problems at European and International level. Many stakeholders have been identified which have committed themselves to the project, a clear indication of the potential impact of the project. The importance for economic and societal sector is also high, for example there may be opportunities to exploit new MST approaches but this aspect is not expanded as opportunities for commercial exploitation are beyond the remit set of the project whose main focus remains water quality assessment.
Projet CONTACT (ANR 2021-2024)
Consequences of antimicrobials and antiparasitics administration in fish farming for aquatic ecosystems (contact : T. Vogel). Aquaculture is an important source for food, nutrition, income and livelihoods for millions of people around the globe. Intensive fish farming is often associated with pathogen outbreaks and therefore high amounts of veterinary drugs are used worldwide. As in many other environments, mostly application of antimicrobials triggers the development of (multi)resistant microbiota. This process might be fostered by co-selection as a consequence of the additional use of antiparasitics. Usage of antimicrobials in aquaculture does not only affect the cultured fish species, but - to a so far unknown extent - also aquatic ecosystems connected to fish farms including microbiota from water and sediment as well as its eukaryotes. Effects include increases in the number of (multi)resistant microbes, as well as complete shifts in microbial community structure and function. This dysbiosis might have pronounced consequences for the functioning of aquatic ecosystems. Thus in the frame of this project we want to study consequences of antimicrobial/ parasitic application in aquaculture for the cultured fish species as well as for the aquatic environments. To consider the variability of aquaculture practices worldwide four showcases representing typical systems from the tropics, the Mediterranean and the temperate zone will be studied including freshwater and marine environments. For one showcase a targeted mitigation approach to reduce the impact on aquatic ecosystems will be tested.
The project delivers in depth understanding of the underlying mechanisms of ARG dissemination from aquaculture due to veterinary drugs application. Outcomes will benefit society, as to contribute to raise awareness of a potential co-selection of veterinary drugs in fish farming, and define necessary countermeasures to be taken for more sustainable aquaculture practices (hence competitiveness.
The immediate impact of the enhancement of innovation capacity, or in creating new market opportunities is not tangible from this proposal, which is however implemented to understand the mechanisms of potential spreading of antimicrobial resistance genes and not solving this issue. The expected results and the knowledge acquired during the project development will be of importance for economic sector of fish farming and also for the society since more information about the possible presence and spreading of antimicrobial resistance genes would make more awareness in the end consumers.
Projet EiCLaR (H2020 2021-2024)
Enhanced In situ bioremediation for Contaminated Land Remediation (contact : T. Vogel). EiCLaR, as a EU/China consortium, will develop scientific and technical innovations for in situ bioremediation technologies that will be directly developed into industrial processes for the rapid efficient cost-effective treatment of a range of environmental pollutants such as chlorinated solvents, heavy metals, pesticides, etc. These technologies (Electro-nanobioremediation, innovative Bioaugmentation, Bioelectrochemical remediation, Enhanced phytoremediation) will enable bioremediation approaches to expand their range of applications to industrial sites and waters that contain complex, high concentration pollutant mixtures. This project will move our proof-of-concept level advances to industrial commercial processes through laboratories studies to refine the processes and to explore the scientific base and scale-up techniques and field demonstrations. Our recent advances in nanobioremediation will be enhanced by studies of the critical microbial component and the use of electrochemical processes to increase the degradation rate and biocatalyst lifetime. The innovative bioaugmentation is based on a recently discovered bacteria capable of degrading some chlorinated solvents efficiently under aerobic conditions. The Bioelectrochemical system will speed up the anaerobic degradation of pollutants when aeration is not feasible. The enhanced phytoremediation will benefit from the synergistic effect of fungi and electrokinetic nutrient dispersion. These environmental sustainable and low impact depollution methods will provide service companies with the tools to manage contaminated soil and water and improve environmental quality at over a million sites throughout Europe and China. These companies will be able to grow by increased personnel and revenue while improving biodiversity and reducing environmental risks. https://eiclar.eu
